Abstract

Using Monte Carlo simulations of a touching-bead model of double-stranded DNA, we show that DNA extension is enhanced in isosceles triangular nanochannels (relative to a circular nanochannel of the same effective size) due to entropic depletion in the channel corners. The extent of the enhanced extension depends non-monotonically on both the accessible area of the nanochannel and the apex angle of the triangle. We also develop a metric to quantify the extent of entropic depletion, thereby collapsing the extension data for circular, square, and various triangular nanochannels onto a single master curve for channel sizes in the transition between the Odijk and de Gennes regimes.

Received 21 January 2013Accepted 14 February 2013Published online 01 March 2013

Acknowledgments:

We thank Professor Shuichi Takayama (University of Michigan) for sharing his experimental insights into this problem. This work was supported by the NIH (R01-HG005216) and was carried out in part using computing resources at the University of Minnesota Supercomputing Institute.